LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-296-g061c80104a-modified)
  using 1 OpenMP thread(s) per MPI task
# Aspherical shear demo - 2d line boxes, solvated by SRD particles

units           lj
atom_style      line
atom_modify     first big
dimension       2

read_data       data.line.srd
Reading data file ...
  orthogonal box = (-28.796757 -28.796757 -0.5) to (28.796757 28.796757 0.5)
  4 by 2 by 1 MPI processor grid
  reading atoms ...
  400 atoms
  400 lines
  read_data CPU = 0.002 seconds

# add small particles as hi density lattice

lattice         sq 0.4
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
region          plane block INF INF INF INF -0.001 0.001
lattice         sq 10.0
Lattice spacing in x,y,z = 0.31622777 0.31622777 0.31622777
create_atoms    2 region plane
Created 33489 atoms
  using lattice units in orthogonal box = (-28.796757 -28.796757 -0.5) to (28.796757 28.796757 0.5)
  create_atoms CPU = 0.001 seconds

group           big type 1
400 atoms in group big
group           small type 2
33489 atoms in group small
set             group small mass 0.01
Setting atom values ...
  33489 settings made for mass

# delete overlaps
# must set 1-2 cutoff to non-zero value

pair_style      lj/cut  1.5
pair_coeff      1 1 1.0 1.0
pair_coeff      2 2 0.0 1.0 0.0
pair_coeff      1 2 1.0 1.0

delete_atoms    overlap 1.5 small big
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.8
  ghost atom cutoff = 1.8
  binsize = 0.9, bins = 64 64 2
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) command delete_atoms, occasional
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/2d
      bin: standard
  (2) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d
      bin: standard
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:313)
Deleted 13605 atoms, new total = 20284

# SRD run

reset_timestep  0

velocity        small create 1.44 87287 loop geom

neighbor        0.8 multi
neigh_modify    delay 0 every 1 check yes
neigh_modify    exclude molecule/intra big include big

comm_modify     mode multi group big vel yes
neigh_modify    include big

# no pairwise interactions with small particles

pair_style      line/lj 2.5
pair_coeff      1 1 1.0  1.0 1.0 1.0 2.5
pair_coeff      2 2 0.0  0.0 0.0 1.0 0.0
pair_coeff      1 2 1.0  0.2 1.0 0.2 2.5

# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles

timestep        0.0002

fix             1 big rigid molecule
  100 rigid bodies with 400 atoms
fix             2 small srd 20 big 1.0 0.25 49894                 search 0.2 cubic warn 0.0001 shift yes 49829                 overlap yes collision noslip

fix             3 all deform 1 x scale 1.25 y scale 1.25
fix             4 all enforce2d

# diagnostics

compute         tsmall small temp/deform
compute         tbig big temp
variable        pebig equal pe*atoms/count(big)
variable        ebig equal etotal*atoms/count(big)

compute_modify  tbig extra/dof -350

compute         1 big erotate/asphere
compute         2 all ke
compute         3 all pe
variable        toteng equal (c_1+c_2+c_3)/atoms

thermo          1000
thermo_style    custom step c_tsmall f_2[9] c_1 etotal                 v_pebig v_ebig press
thermo_modify   temp tbig
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:533)

compute         10 big property/atom end1x end1y end2x end2y

#dump           1 all custom 500 dump1.atom.srd id type x y z ix iy iz
#dump           2 all custom 500 dump1.line.srd id type #               c_10[1] c_10[2] c_10[3] c_10[4]

run             10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419

@Article{Gissinger24,
 author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
 title = {Type Label Framework for Bonded Force Fields in LAMMPS},
 journal = {J. Phys. Chem. B},
 year =    2024,
 volume =  128,
 number =  13,
 pages =   {3282–-3297}
}

- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2

@Article{Intveld08,
 author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
 title =   {Accurate and Efficient Methods for Modeling Colloidal
            Mixtures in an Explicit Solvent using Molecular Dynamics},
 journal = {Comput.\ Phys.\ Commut.},
 year =    2008,
 volume =  179,
 pages =   {320--329}
}

@article{Shire2020,
 author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
 title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
          Detection Applied to Investigate the Quasi-Static Limit},
 journal = {Computational Particle Mechanics},
 year = {2020}
@article{Monti2022,
 author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava, 
           Ishan and Silbert, Leonardo E. and Grest, Gary S. 
           and Lechman, Jeremy B.},
 title = {Large-scale frictionless jamming with power-law particle 
          size distributions},
 journal = {Phys. Rev. E},
 volume = {106}
 issue = {3}
 year = {2022}
}

- fix srd command: doi:10.1063/1.3419070

@Article{Petersen10,
 author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
 G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
 title =   {Mesoscale Hydrodynamics via Stochastic Rotation
    Dynamics: Comparison with {L}ennard-{J}ones Fluid},
 journal = {J.~Chem.\ Phys.},
 year =    2010,
 volume =  132,
 pages =   174106
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Using compute temp/deform with inconsistent fix deform remap option (src/compute_temp_deform.cpp:71)
WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405)
SRD info:
  SRD/big particles = 19884 400
  big particle diameter max/min = 1.9988171 0.50330564
  SRD temperature & lamda = 1 0.04
  SRD max distance & max velocity = 0.16 40
  SRD grid counts: 230 230 1
  SRD grid size: request, actual (xyz) = 0.25, 0.25040659 0.25040659 1
  SRD per actual grid cell = 0.45503978
  SRD viscosity = 1.0732692
  big/SRD mass density ratio = 12.298053
WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
  # of rescaled SRD velocities = 0
  ave/max small velocity = 15.906001 29.105426
  ave/max big velocity = 0 0
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 3.3
  ghost atom cutoff = 3.3
  binsize = 1.65, bins = 35 35 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair line/lj, perpetual
      attributes: half, newton on
      pair build: half/multi/atomonly/newton
      stencil: half/multi/2d
      bin: multi
Per MPI rank memory allocation (min/avg/max) = 9.752 | 9.762 | 9.781 Mbytes
   Step        c_tsmall        f_2[9]          c_1           TotEng        v_pebig         v_ebig         Press     
         0   1.4809886      0              0              0              0              0              0            
      1000   1.2265081      1.1522909      0.00027866069  0.0022427232   0              0.1137285      0.58262976   
      2000   1.1757141      1.1251323      0.00040597152  0.003287261    0              0.16669701     0.27109853   
      3000   1.126304       1.0646585      0.00050542958  0.0040748897   0              0.20663766     0.36959653   
      4000   1.1140297      1.0761435      0.00060430927  0.0052863645   0              0.26807154     0.35099205   
      5000   1.0823307      1.0256814      0.00066557681  0.0051213284   0              0.25970256     0.28491631   
      6000   1.0656188      1.0387091      0.00066454105  0.005213537    0              0.26437846     0.2150581    
      7000   1.0600108      1.0099931      0.0007238719   0.005470459    0              0.27740698     0.21846568   
      8000   1.0464374      1.0049819      0.00061068366  0.0053702582   0              0.27232579     0.1326171    
      9000   1.0381097      1.0126049      0.00057318728  0.0055976321   0              0.28385592     0.16797796   
     10000   1.0312982      1.0018962      0.00050597007  0.0051153126   0              0.2593975      0.15281043   
Loop time of 1.2997 on 8 procs for 10000 steps with 20284 atoms

Performance: 132953.355 tau/day, 7694.060 timesteps/s, 156.066 Matom-step/s
96.7% CPU use with 8 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.01406    | 0.014495   | 0.01532    |   0.3 |  1.12
Neigh   | 0.0051916  | 0.0053424  | 0.0054386  |   0.1 |  0.41
Comm    | 0.062053   | 0.065305   | 0.069014   |   0.9 |  5.02
Output  | 0.00062289 | 0.00065254 | 0.00077243 |   0.0 |  0.05
Modify  | 1.169      | 1.178      | 1.1905     |   0.6 | 90.64
Other   |            | 0.03589    |            |       |  2.76

Nlocal:         2535.5 ave        2637 max        2476 min
Histogram: 1 3 1 1 0 0 0 0 1 1
Nghost:         31.125 ave          42 max          25 min
Histogram: 3 0 1 2 0 0 0 0 1 1
Neighs:              0 ave           0 max           0 min
Histogram: 8 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 500
Dangerous builds = 0

#undump          1
#undump          2
unfix           3

change_box      all triclinic
Changing box ...
  triclinic box = (-35.995947 -35.995947 -0.5) to (35.995947 35.995947 0.5) with tilt (0 0 0)

fix             2 small srd 20 big 1.0 0.25 49894                 search 0.2 cubic warn 0.0001 shift yes 49829                 overlap yes collision noslip #tstat yes

#dump           1 all custom 500 dump2.atom.srd id type x y z ix iy iz
#dump           2 all custom 500 dump2.line.srd id type #               c_10[1] c_10[2] c_10[3] c_10[4]

fix             3 all deform 1 xy erate 0.0002 units box remap v

run             40000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405)
SRD info:
  SRD/big particles = 19884 400
  big particle diameter max/min = 1.9988171 0.50330564
  SRD temperature & lamda = 1 0.04
  SRD max distance & max velocity = 0.16 40
  SRD grid counts: 288 288 1
  SRD grid size: request, actual (xyz) = 0.25, 0.24997185 0.24997185 1
  SRD per actual grid cell = 0.26976265
  SRD viscosity = 1.5799049
  big/SRD mass density ratio = 20.672578
WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809)
WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830)
  # of rescaled SRD velocities = 1
  ave/max small velocity = 12.481632 40
  ave/max big velocity = 0.58815233 1.5489134
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 3.3
  ghost atom cutoff = 3.3
  binsize = 1.65, bins = 44 44 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair line/lj, perpetual
      attributes: half, newton on
      pair build: half/multi/atomonly/newton/tri
      stencil: half/multi/2d/tri
      bin: multi
Per MPI rank memory allocation (min/avg/max) = 11.95 | 11.95 | 11.95 Mbytes
   Step        c_tsmall        f_2[9]          c_1           TotEng        v_pebig         v_ebig         Press     
     10000   0.98889306     0              0.00050595647  0.0051153289   0              0.25939833     0.020019811  
     11000   0.98995417     0.99721412     0.0005166709   0.0054320552   0              0.27545952     0.03376188   
     12000   0.99401168     0.95502319     0.00053659416  0.0054974426   0              0.27877531     0.056856034  
     13000   0.98790692     0.96488357     0.00061076364  0.0053196554   0              0.26975972     0.2677228    
     14000   0.98939233     0.98809694     0.00052317779  0.0050536922   0              0.25627273     0.20381427   
     15000   0.99046365     0.97048828     0.00056914402  0.0053274908   0              0.27015706     0.082163088  
     16000   0.99743447     1.0111983      0.00053706165  0.0048068384   0              0.24375478     0.06429569   
     17000   0.99622359     1.0124982      0.0005905197   0.0055966416  -7.4541903e-05  0.2838057      0.25418037   
     18000   0.99283929     0.99581721     0.00061730878  0.0059098964  -0.00014754106  0.29969084     0.12701702   
     19000   0.99175517     1.0115581      0.0005128714   0.0059214809  -0.00046203987  0.30027829     0.2640506    
     20000   0.98895811     0.97731528     0.00052294314  0.0055670021  -0.0016029702   0.28230268     0.26239209   
     21000   0.98904093     0.98120258     0.00054169978  0.0052762731  -0.0026834879   0.26755981     0.15432481   
     22000   0.98773149     0.99217218     0.00056091602  0.0052754729  -0.0044093345   0.26751923     0.2208051    
     23000   0.98802862     0.96564549     0.00062226338  0.0053263454  -0.008790914    0.27009898     0.18058977   
     24000   0.98754002     1.024015       0.00057178953  0.0054083382  -0.0094859317   0.27425683     0.01598147   
     25000   0.98656341     0.94647246     0.00066215791  0.0053555849  -0.014877058    0.27158171     0.28794628   
     26000   0.98750471     1.0077626      0.00058955769  0.0057081639  -0.013151869    0.28946099     0.20814911   
     27